The origin of genetic variation

The origin of genetic variationI. Motivation

Evolution is a change in the genotype of the population over time. Phenotypic differences between species reflects genetic differences between species = genetic variation across species

What is the origin of genetic variation??Ultimate Source:MUTATION!!!!!!!!!!!!!!!!!!!!!!!!!!!!

All populations demonstrate phenotypic variation, some of which is due to genetic variation

Sonora seiminanulata

Asterina miniata

Linantus ciliatus

II. Origin genetic variation: What is a mutation???-offspring has DNA that is different from both parents-deleterious alleles in population are often referred to as mutations

Mutation = change in nucleotide, deletion, insertion, duplication, inversion….

mRNA

Note: Genetic Redundancy of Code Results in Synonymous & NonSynonymous Mutations for Protein Coding Regions

Transitions are more common than transversions becauseDNA repair enzymes can recognize wrong insertion representing a a transition better than a transversion

Common molecular mechanisms resulting in mutation

III. Properties of Mutations:

Random

What are the effects of new (deletion) mutations? Deleterious? Strong?

s = 1 – fitness(mutation)/fitness(without mutation)Fitness of genotype with mutation = 1 - s

RATES: How do you measure mutation rates at the DNA LEVEL?

Direct sequencing of C. elegans Mutation Accumulation Lines

Denver et al. 2004

. . .

. . .

Generation 280: 29,561 bp in 72 MA linesGeneration 353: 14,550 bp in 68 MA linesGeneration 396: 18,718 bp in 58 MA lines

Detected: 30 mutations (17/30 indels)Transitions >> Transversions 1.6:1

Mutation rate: 2.1 x 10-8 /site/generation400 generations= about 1 mutation/gamete or 2/zygote

Figure 5-34

Mutation Rates Generally Low

And can evolve

Mutation accumulation lines

Homozygous progenitor

Mutation accumulation lines

Singleseeddescent

Any genetic differences between lines = mutations

Current project: extending MA research to field studies

planted at 4 leaf rosette stage

Field Site After Planting100 lines(25th generation of MA) x 70 Replicates/line = 7000 + 500 parentals (founders) = 7500 plants

Site 8 weeks later at harvest

Herbivory

Total fruit produced= fruit # * survival

0

2

4

6

8

10

12

14

9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

Fruit number

# of

MA

line

s

MA lines have diverged in fitnessFounder performance is near the

average MA performance

Block <0.0001MA line 0.029 MA line vs. Founder 0.8650Subline 0.0051

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana, Ossowski et al., 2010, Science, 1 January

• Conducted 30 generations of MA

• Screened 5 MA lines (we tested for performance)

• Detected 114 mutations

• Mutation Rate: 30 x 5 = 150 episodes 111 mutations/150 ~ 1.4 mutations per diploid or zygote generation Each line ~ 20 mutations

Accuracy: about 1 new mutation for every 200 mbp replicated

Mutations Detected

Dark blue lines are mutations in coding regions

Comparison of Mutation Rate at Sequence Level vs.

PerformanceFor each new zygote:

1.4 mutations at the sequence level 0.24 mutation rate for performance About 20% of mutations effect performance About 80% of mutations have no effect on performance About 20% of all sequence mutations were nonsynonymous and in coding regions

Rutter et al., Evolution, 2012

Beginning of a conceptual framework for the prediction of mutation effects

(with Jon Agren, Thomas Lenormand, Eric Imbert, Detlef Weigel &Stephen Wright)

Adaptive landscapes & mutation parameters

Fisher, 1930

New MA lines fromSweden and France

IV. Origin of new loci/function: Gene Duplication

Timing of expression differs among members of the globin gene families

Paralogs- loci that diverge following duplicationOrthologs- loci that are homologous then diverge following speciationPseudogenes- class of genes that have no function (non-transcribed)

O

P

Homologous genes come in one of two types:

Importance of gene duplication to evolution? VERY

V. Chromosome Inversions

Suppress recombination

inversions can keep gene combinations intact, eg.

A/abcdE/e

AND THE EVOLUTIONARY IMPORTANCE?????????

Evidence that inversions are associated with adaptation

ALSO LINKAGE DISEQUILIBRIUM WITHIN INVERSION

in Drosophila subobscura

Figure 1. Geographic distribution of the chromosomal inversion. (A) Map of western North America with the locations of populations ofcoastal perennials (blue), inland annuals (orange), and inland perennials (purple), as well as obligate self-fertilizing species M. nasutus (yellow). (B) Marker order of the AN and PE inversion arrangements along linkage group eight. Inland annuals and M. nasutus had the AN arrangement whilecoastal and inland perennials all had the PE arrangement.

doi:10.1371/journal.pbio.1000500.g001Adaptive Inversion Contributes to IsolationPLoS Biology | www.plosbiology.org 3 September 2010 | Volume 8 | Issue 9 | e1000500

Mimulus guttatus

Figure 2. Replicated effect of the inversion locus. (A) F2 progeny with parental ecotypic phenotypes, from a cross between the SWB (coastalperennial) and LMC (inland annual) populations. (B–E) Effect of the inversion on flowering time in four independently derived F2 mappingpopulations created through crosses between independent inland annual and coastal perennial populations. (F) Effects of the inversion on floweringtime in cross between inland annual and inland perennial populations. The mean flowering times (61 SE) of F2s that were homozygous for the ANarrangement (AA), heterozygous (AB), and homozygous for the PE arrangement (BB) at Micro6046 are indicated. The percentage of F2 variance/parental divergence explained by the inversion is presented above each bar graph. Note: y-axes do not originate at zero.doi:10.1371/journal.pbio.1000500.g002

VI. Polyploidy

duplication ofthe basic numberof chromosomes,

e.g.: 2n to 3 n to 4n etc.,

Results in instant speciation

Common, in plants Why?

Answ: meiosis exposed, sex chromo. rare, selfing frequent.

And others: Translocation, transposable elements…

Gene Duplication and Adaptation:Variation, Survivorship in a common garden in dunes and flowering time distributions of yarrow with different ploidy

VII. Much variation in populations

• Heterozygosity: average frequency of heterozygotes across loci

• Proportion of loci polymorphic

Vertebrates

The distribution of enzyme heterozygosities among species of animals and plants

Fraction of loci that are heterozygous in the genotype of the average individual

Sequencing studies have revealed enormous genetic diversity at the cystic fibrosis locus in humans.

Loss of function mutations found in humans with cystic fibrosis

Figure 5-7

Offspring of two Heterozygotes for TAS2R38, PAV and AVI alleles

*AVI/AVI individuals cannot taste bitter taste of broccolli = vegetarians

http://www.nature.com/nature/journal/v486/n7403_supp/full/486S16a.html

Calculating Heterozygosity:

Determining CCR5 genotypes by electrophoresis of DNA

Origin of fragment size: shorter by 32 nuc.

16/43= 0.37 (Hets)

F(D32)=

16 + 2x1 = 18

18/86= 0.21

Conclusion

• Mutation rates are high• Mutations effect fitness• Mutations contribute to genetic variation• Duplications can lead to new gene

function• Inversions can protect adaptations• Polyploidy can result in instant

speciation• Mutations are important to evolution